Can some one explain to what happens when RTG is used in UAE?
I assume it is bypassing the chipset. How does this affect the speed and can it talk to hardware directly? Does it still go through the Host OS?
Thanks.

As far as I know, the RTG mode simply provides a software "chip" driver for Picasso96 that uses the underlying host OS to do the blitter accelerated stuff. The host OS in turn may use hardware acceleration for said operations.

The native chipset stuff is still emulated too but I imagine there's plenty of shortcut optimisations that can be made when said chipset isn't displaying anything.

Amithlon is built from UAE with a stripped down and patched Linux, so they are very similar.

Graphics wise, assuming that you are running on the same hardware, Amithlon will be a little faster because it translate most of the calls directly to video card specific, accelerated calls.

On modern hardware, E-UAE can be as fast or faster because the hardware can be fast enough to negate the advantage of more direct calls on slower older hardware.

The real advantage to Amithlon that is rarely used is the ability to have native PCI access to cards and using apps that have some native Intel code in them.  

You could do some of this with various old versions of UAE as well, but they weren't as polished and have slowly been removed or left in states that might or might not work.

The other advantage is that Amithlon covers up the host OS, making it seem more like a fast Amiga than an emulation.